Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF QUINOHEMOPROTEIN ALCOHOL DEHYDROGENASE FROM COMAMONAS TESTOSTERONI
 
Authors :  H. J. Rozeboom, A. Oubrie
Date :  05 Nov 01  (Deposition) - 28 Dec 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.44
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Propeller Fold, Cytochrome C, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Oubrie, H. J. Rozeboom, K. H. Kalk, E. G. Huizinga, B. W. Dijkstra
Crystal Structure Of Quinohemoprotein Alcohol Dehydrogenase From Comamonas Testosteroni: Structural Basis For Substrate Oxidation And Electron Transfer.
J. Biol. Chem. V. 277 3727 2002
PubMed-ID: 11714714  |  Reference-DOI: 10.1074/JBC.M109403200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - QUINOHEMOPROTEIN ALCOHOL DEHYDROGENASE
    ChainsA
    EC Number1.1.99.-
    Organism ScientificCOMAMONAS TESTOSTERONI
    Organism Taxid285
    SynonymQUINOHEMOPROTEIN ETHANOL DEHYDROGENASE TYPE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 8)

Asymmetric/Biological Unit (6, 8)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2GOL3Ligand/IonGLYCEROL
3HEC1Ligand/IonHEME C
4PQQ1Ligand/IonPYRROLOQUINOLINE QUINONE
5TFB1Ligand/IonTETRAHYDROFURAN-2-CARBOXYLIC ACID
6TRO1Mod. Amino Acid2-HYDROXY-TRYPTOPHAN

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:185 , ASN A:263 , ASP A:308 , PQQ A:1800 , TFB A:1810BINDING SITE FOR RESIDUE CA A 801
2AC2SOFTWAREARG A:67 , GLN A:435 , ASN A:603 , CYS A:604 , CYS A:607 , HIS A:608 , PRO A:620 , MET A:625 , TYR A:629 , LEU A:633 , PHE A:636 , PRO A:641 , ALA A:642 , ARG A:645 , GLY A:646 , MET A:647 , PRO A:648 , PHE A:650 , HOH A:2067 , HOH A:2541 , HOH A:2726BINDING SITE FOR RESIDUE HEC A 802
3AC3SOFTWARECYS A:116 , CYS A:117 , GLU A:185 , TRP A:267 , ASP A:308 , PRO A:389 , TRP A:440 , CA A:801 , PQQ A:1800 , HOH A:2840BINDING SITE FOR RESIDUE TFB A 1810
4AC4SOFTWAREGLU A:70 , CYS A:116 , CYS A:117 , VAL A:120 , ARG A:122 , THR A:167 , GLY A:182 , GLY A:183 , ALA A:184 , GLU A:185 , THR A:243 , TRP A:245 , ASN A:263 , ASP A:308 , LYS A:335 , ASN A:394 , TRP A:395 , TRP A:479 , GLY A:543 , VAL A:544 , CA A:801 , TFB A:1810 , HOH A:1845 , HOH A:1856BINDING SITE FOR RESIDUE PQQ A 1800
5AC5SOFTWAREGLU A:474 , HIS A:475 , ARG A:499 , TYR A:503 , LYS A:510 , HOH A:1866 , HOH A:2611BINDING SITE FOR RESIDUE GOL A 1820
6AC6SOFTWARETRP A:541 , ARG A:550 , THR A:552 , ARG A:554 , GLN A:555 , GLY A:617 , ASN A:618 , HOH A:1913 , HOH A:1945 , HOH A:2575BINDING SITE FOR RESIDUE GOL A 1823
7AC7SOFTWAREHOH A:2447 , HOH A:2635BINDING SITE FOR RESIDUE GOL A 1824

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:116 -A:117

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser A:265 -Pro A:266
2Leu A:280 -Tyr A:281
3Val A:386 -Pro A:387

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KB0)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BACTERIAL_PQQ_2PS00364 Bacterial quinoprotein dehydrogenases signature 2.QHED_COMTE276-297  1A:245-266
2CYTCPS51007 Cytochrome c family profile.QHED_COMTE622-701  1A:591-670

(-) Exons   (0, 0)

(no "Exon" information available for 1KB0)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:670
 aligned with QHED_COMTE | Q46444 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:675
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701     
           QHED_COMTE    32 TGPAAQAAAAVQRVDGDFIRANAARTPDWPTIGVDYAETRYSRLDQINAANVKDLGLAWSYNLESTRGVEATPVVVDGIMYVSASWSVVHAIDTRTGNRIWTYDPQIDRSTGFKGCCDVVNRGVALWKGKVYVGAWDGRLIALDAATGKEVWHQNTFEGQKGSLTITGAPRVFKGKVIIGKRGAEYGVRGYITAYDAETGERKWRWFSVPGDPSKPFEDESMKRAARTWDPSGKWWEAGGGGTMWDSMTFDAELNTMYVGTGNGSPWSHKVRSPKGGDNLYLASIVALDPDTGKYKWHYQETPGDNWDYTSTQPMILADIKIAGKPRKVILHAPKNGFFFVLDRTNGKFISAKNFVPVNWASGYDKHGKPIGIAAARDGSKPQDAVPGPYGAHNWHPMSFNPQTGLVYLPAQNVPVNLMDDKKWEFNQAGPGKPQSGTGWNTAKFFNAEPPKSKPFGRLLAWDPVAQKAAWSVEHVSPWNGGTLTTAGNVVFQGTADGRLVAYHAATGEKLWEAPTGTGVVAAPSTYMVDGRQYVSVAVGWGGVYGLAARATERQGPGTVYTFVVAGKARMPEFVAQRTGQLLQGVKYDPAKVEAGTMLYVANCVFCHGVPGVDRGGNIPNLGYMDASYIENLPNFVFKGPAMVRGMPDFTGKLSGDDVESLKAFIQGTADAIRP 706
               SCOP domains d1kb0a2 A:1-573 Quinoprotein alcohol dehydrogenase, N-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        -----d1kb0a1 A:579-675 Quinoprotein alcohol dehydrogenase, C-terminal domain                           SCOP domains
               CATH domains 1kb0A01 A:1-580  [code=2.140.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                1kb0A02 A:581-675 Cytochrome c                                                                  CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PQQ-1kb0A01 A:488-526                  ----------------------------------------------------------------Cytochrome_CBB3-1kb0A06 A:591-666                                           --------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PQQ-1kb0A02 A:488-526                  ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PQQ-1kb0A03 A:488-526                  ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PQQ-1kb0A04 A:488-526                  ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
           Pfam domains (5) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PQQ-1kb0A05 A:488-526                  ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (5)
         Sec.struct. author hhhhhhhhhhhhh.hhhhhhhhhhh...............ee........hhhhheeeeeee...........eee..eeeee.hhh.eeeee.....eeeee....hhhhhhhh.........eee..eeeee....eeeeee.....eeeeee...............eee..eeee...........eeeeee.....eeeeee...........hhhhhhhhhhhhhhhh.....ee......eeee....eeeee...ee..hhhhhh..........eeeee......eeeeee...............eeeeeee..eeeeeeee.....eeeeee.....eeeeee......eeee.....eee.hhhhh....ee..............eee....eeeeeeee...eeee..............hhhhh....eee.........eeeeeeee....eeeeeeee.......eeee...eeeee....eeeeee.....eeeeee.........eeeee..eeeeeeee..hhhhhhhh.........eeeeee.........-----..........hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh...hhhhh..........hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BACTERIAL_PQQ_2       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTC  PDB: A:591-670 UniProt: 622-701                                           ----- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kb0 A   1 TGPAAQAAAAVQRVDGDFIRANAARTPDWPTIGVDYAETRYSRLDQINAANVKDLGLAWSYNLESTRGVEATPVVVDGIMYVSASWSVVHAIDTRTGNRIWTYDPQIDRSTGFKGCCDVVNRGVALWKGKVYVGAWDGRLIALDAATGKEVWHQNTFEGQKGSLTITGAPRVFKGKVIIGNGGAEYGVRGYITAYDAETGERKWRWFSVPGDPSKPFEDESMKRAARTWDPSGKWWEAGGGGTMWDSMTFDAELNTMYVGTGNGSPWSHKVRSPKGGDNLYLASIVALDPDTGKYKWHYQETPGDNWDYTSTQPMILADIKIAGKPRKVILHAPKNGFFFVLDRTNGKFISAKNFVPVNWASGYDKHGKPIGIAAARDGSKPQDAVPGPYGAHNWHPMSFNPQTGLVYLPAQNVPVNLMDDKKWEFNQAGPGKPQSGTGWNTAKFFNAEPPKSKPFGRLLAWDPVAQKAAWSVEHVSPWNGGTLTTAGNVVFQGTADGRLVAYHAATGEKLwEAPTGTGVVAAPSTYMVDGRQYVSVAVGWGGVYGLAARATERQGPGTVYTFVVGGKARMPE-----TGQLLQGVKYDPAKVEAGTMLYVANCVFCHGVPGVDRGGNIPNLGYMDASYIENLPNFVFKGPAMVRGMPDFTGKLSGDDVESLKAFIQGTADAIRP 675
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510 |     520       530       540       550       560       570  |    580       590       600       610       620       630       640       650       660       670     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         512-TRO                                                      573   579                                                                                                

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 6)

Asymmetric/Biological Unit

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (QHED_COMTE | Q46444)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016614    oxidoreductase activity, acting on CH-OH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PQQ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TFB  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TRO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:280 - Tyr A:281   [ RasMol ]  
    Ser A:265 - Pro A:266   [ RasMol ]  
    Val A:386 - Pro A:387   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1kb0
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  QHED_COMTE | Q46444
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.1.99.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  QHED_COMTE | Q46444
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 1KB0)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1KB0)